The Archon class remains hilariously unnecessary (the first usage of it should be Keter, the second Thaumiel), and some of the psychic gobbledegook could have been trimmed down, but I very much enjoyed the framing device and the plot.

While the first usage could be Keter, that would come at the cost of losing the impact of the third object class (Keter-Neutralised-Keter) doesn't have the same punch. Also, on a meta level, if Archon is something that we explicitly shouldn't restrict, lest we face dire consequences, then our biosphere and natural habitats are real life Archon entities. (If I'm allowed to be a preachy environmentalist.)

The final usage however explicitly can't be Thaumiel. The Thaumiel class, by definition, is used for anomalies that are used to answer other anomalies. And Gaia mostly exists in isolation.

But the new Claire-Gaia doesn’t exist in isolation - her existence is inexplicably tied to life on Earth as we know it. She is an anomaly needed to contain the anomaly that her nonexistence causes mass extinctions. Hell, she was created by the Foundation. So she has to be Thaumiel.

Her absence leaves us at the default state, and the default state of life is failure (especially once our environmental destruction is considered). This SCP thus proposes that while life itself is not necessarily an anomaly, it's incredible success and propagation is.

While logically your argument is completely correct, and I would normally concede and edit appropriately, I've made these decisions for deliberate thematic reasons.

If it's any consolation, I'll point out that I was considering using the Apollyon class for 4043-B for quite a while.

I absolutely enjoyed and loved this SCP, as well as her awesome AI Helper. I personally like the idea and concept of a Mother Earth that can feel the same emotions and pain as normal humans do, and how our acts of mass pollution and environmental destruction directly impacts her health.
+1 from me. This SCP deserved it :3